35 research outputs found
Environmentally relevant fungicide levels modify fungal community composition and interactions but not functioning
No full textAquatic hyphomycetes (AHs), a group of saprotrophic fungi adapted to submerged leaf litter, play key functional roles in stream ecosystems as decomposers and food source for higher trophic levels. Fungicides, controlling fungal pathogens, target evolutionary conserved molecular processes in fungi and contaminate streams via their use in agricultural and urban landscapes. Thus fungicides pose a risk to AHs and the functions they provide. To investigate the impacts of fungicide exposure on the composition and functioning of AH communities, we exposed four AH species in monocultures and mixed cultures to increasing fungicide concentrations (0, 5, 50, 500, and 2500 mg/L). We assessed the biomass of each species via quantitative real-time PCR. Moreover, leaf decomposition was investigated. In monocultures, none of the species was affected at environmentally relevant fungicide levels (5 and 50 mg/L). The two most tolerant species were able to colonize and decompose leaves even at very high fungicide levels (>= 500 mg/L), although less efficiently. In mixed cultures, changes in leaf decomposition reflected the response pattern of the species most tolerant in monocultures. Accordingly, the decomposition process may be safeguarded by tolerant species in combination with functional redundancy. In all fungicide treatments, however, sensitive species were displaced and interactions between fungi changed from complementarity to competition. As AH community composition determines leaves' nutritional quality for consumers, the data suggest that fungicide exposures rather induce bottom-up effects in food webs than impairments in leaf decomposition. (C) 2021 The Author(s). Published by Elsevier Ltd
Unravelling the enzymatic wood decay repertoire of Cerrena zonata: A multi-omics approach
No full textLignocellulosic biomass (LCB), such as wheat straw, bagasse, or wood, is a cost-effective, sustainable carbon source but remains challenging to utilize due to the recalcitrance of lignin, which hinders efficient carbohydrate hydrolysis. Effective LCB degradation demands a wide range of enzymes, and commercial enzyme cocktails often require physical or chemical pretreatments. A fully enzymatic degradation could drastically improve the efficiency of these processes. Basidiomycota fungi naturally possess diverse enzymes suited for LCB breakdown. The white-rot fungus Cerrena zonata, a member of the phylum Basidiomycota, was analyzed for its Carbohydrate-Active Enzymes (CAZymes) using a multi-omics approach. Genomic and transcriptomic analyses of C. zonata identified 20,816 protein-encoding genes, including 487 CAZymes (2.3 %). Cultivating C. zonata with and without LCB addition revealed a total of 147 proteins, of which 36 were CAZymes (13 auxiliary activities (AA), 3 carbohydrate esterases, and 20 glycoside hydrolases). In accordance, laccase, manganese peroxidase (MnP) as well as versatile peroxidase (VP) activities were detected in the fungal culture supernatants. Furthermore, relevant enzymes were visualized via zymography. Consistent with these results, five putative peroxidases (AA2) and three putative laccases (AA1_1) were identified in all –omics dimensions. Further structure and sequence analysis of AA2 proteins supports that two proteins were classified as VPs and three as MnPs, based on their active and Mn2 + binding sites. In summary, C. zonata possesses a broad enzyme spectrum expressed under varied conditions, highlighting its potential for identifying efficient lignin-degrading enzymes for enzymatic pretreatment of food industry side streams and other LCBs.29
MediaDive: the expert-curated cultivation media database
No full textTalk at the ECCO XL Meeting 2022
Molecular techniques for pathogen identification and fungus detection in the environment
No full textMany species of fungi can cause disease in plants, animals and humans. Accurate and robust detection and quantification of fungi is essential for diagnosis, modeling and surveillance. Also direct detection of fungi enables a deeper understanding of natural microbial communities, particularly as a great many fungi are difficult or impossible to cultivate. In the last decade, effective amplification platforms, probe development and various quantitative PCR technologies have revolutionized research on fungal detection and identification. Examples of the latest technology in fungal detection and differentiation are discussed here
Molecular techniques for pathogen identification and fungus detection in the Environment
No full textMany species of fungi can cause disease in plants, animals and humans. Accurate and robust detection and quantification of fungi is essential for diagnosis, modeling and surveillance. Also direct detection of fungi enables a deeper understanding of natural microbial communities, particularly as a great many fungi are difficult or impossible to cultivate. In the last decade, effective amplification platforms, probe development and various quantitative PCR technologies have revolutionized research on fungal detection and identification. Examples of the latest technology in fungal detection and differentiation are discussed her
Examples of the collection.
No full texta: Fungi from wood (FW57 Humicola sp, FW16.1 Fusarium sp.), b: Fungi from soil (SF25 Talaromyces sp., SF31 Aspergillus section Terrei), c: Fungi from rice straw (FR1 Aspergillus section Flavi, FR27 Trichoderma sp.), d: Fungi from shrimp shell (Fsh102 Aspergillus section Nidulans, Fsh13 Fusarium sp.), e: Fungi from crab shell (FC2 Lasiodiplodia sp., FC7 Penicillium section Lanata-divaricata & Stolkiae), f: Fungi from insects (Fi19 Aspergillus section Flavi, Fi5 Talaromyces sp.), g: Fungi from fruits (FF1 Aspergillus section Flavi, GeoThi Fusarium sp.), h: Fungi from oil environment (FL10 Penicillium section Citrina, FL6 Aspergillus section Terrei), i: Fungi from hot springs (FH3 Aspergillus section Fumigati, FH101 Aspergillus section Nidulans), all on PDA, 5–6 days.</p
Long-read DNA metabarcoding of ribosomal rRNA in the analysis of fungi from aquatic environments
No full textABSTRACTDNA metabarcoding is now widely used to study prokaryotic and eukaryotic microbial diversity. Technological constraints have limited most studies to marker lengths of ca. 300-600 bp. Longer sequencing reads of several 5 thousand bp are now possible with third-generation sequencing. The increased marker lengths provide greater taxonomic resolution and enable the use of phylogenetic methods of classifcation, but longer reads may be subject to higher rates of sequencing error and chimera formation. In addition, most well-established bioinformatics tools for DNA metabarcoding were originally 10 designed for short reads and are therefore not suitable. Here we used Pacifc Biosciences circular consensus sequencing (CCS) to DNA-metabarcode environmental samples using a ca. 4,500 bp marker that included most of the eukaryote ribosomal SSU and LSU rRNA genes and the ITS spacer region. We developed a long-read analysis pipeline that reduced error rates to levels 15 comparable to short-read platforms. Validation using fungal isolates and a mock community indicated that our pipeline detected 98% of chimeras de novo i.e., even in the absence of reference sequences. We recovered 947 OTUs from water and sediment samples in a natural lake, 848 of which could be classifed to phylum, 486 to family, 397 to genus and 330 to species. By 20 allowing for the simultaneous use of three global databases (Unite, SILVA, RDP LSU), long-read DNA metabarcoding provided better taxonomic resolution than any single marker. We foresee the use of long reads enabling the cross-validation of reference sequences and the synthesis of ribosomal rRNA gene databases. The universal nature of the rRNA operon and our recovery of >100 25 non-fungal OTUs indicate that long-read DNA metabarcoding holds promise for the study of eukaryotic diversity more broadly.</jats:p
Supplementary material 4 from: Nilsson R, Taylor A, Adams R, Baschien C, Bengtsson-Palme J, Cangren P, Coleine C, Daniel H, Glassman S, Hirooka Y, Laszlo I, Iršėnaitė R, Martin-Sanchez P, Meyer W, Oh S, Sampaio J, Seifert K, Sklenář F, Dirk Stubbe D, Suh S, Summerbell R, Svantesson S, Unterseher M, Visagie C, Weiss M, Woudenberg J, Wurzbacher C, Van den Wyngaert S, Yilmaz N, Yurkov A, Kõljalg U, Abarenkov K (2017) Taxonomic annotation of public fungal ITS sequences from the built environment – a report from an April 10-11, 2017 workshop (Aberdeen, UK). . https://doi.org/10.3897/mycokeys.27.20887
No full textFigure 1 from: Nilsson R, Taylor A, Adams R, Baschien C, Bengtsson-Palme J, Cangren P, Coleine C, Daniel H, Glassman S, Hirooka Y, Laszlo I, Iršėnaitė R, Martin-Sanchez P, Meyer W, Oh S, Sampaio J, Seifert K, Sklenář F, Dirk Stubbe D, Suh S, Summerbell R, Svantesson S, Unterseher M, Visagie C, Weiss M, Woudenberg J, Wurzbacher C, Van den Wyngaert S, Yilmaz N, Yurkov A, Kõljalg U, Abarenkov K (2017) Taxonomic annotation of public fungal ITS sequences from the built environment – a report from an April 10-11, 2017 workshop (Aberdeen, UK). . https://doi.org/10.3897/mycokeys.27.20887
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